Per chromosome imputation report for cohort Group1.
Chromosome index, 23 in total. Skip to the section for a particular chromosome using the buttons below.
Information captured during the processing of this cohort.
| Property | Value |
|---|---|
| FORMAT | MINIMAC2 |
| UPLOADED | 31.5.2021 |
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 7206299 | 61.045 |
| 0.1 | 1217154 | 10.311 |
| 0.2 | 808657 | 6.850 |
| 0.3 | 618825 | 5.242 |
| 0.4 | 496358 | 4.205 |
| 0.5 | 408199 | 3.458 |
| 0.6 | 347229 | 2.941 |
| 0.7 | 293101 | 2.483 |
| 0.8 | 246063 | 2.084 |
| 0.9 | 163056 | 1.381 |
| Total | 11804941 | 100.000 |
Variants binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.3 | 320124 | 2.712 |
| 0.4 | 341746 | 2.895 |
| 0.5 | 430708 | 3.649 |
| 0.6 | 657091 | 5.566 |
| 0.7 | 1041515 | 8.823 |
| 0.8 | 1756587 | 14.880 |
| 0.9 | 7228502 | 61.233 |
| 1.0 | 28668 | 0.243 |
| Total | 11804941 | 100.000 |
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by alternate allele frequency
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 547835 | 61.5312 |
| 0.1 | 89887 | 10.0958 |
| 0.2 | 57402 | 6.4472 |
| 0.3 | 45924 | 5.1580 |
| 0.4 | 37597 | 4.2228 |
| 0.5 | 30402 | 3.4147 |
| 0.6 | 27328 | 3.0694 |
| 0.7 | 21847 | 2.4538 |
| 0.8 | 18652 | 2.0949 |
| 0.9 | 13463 | 1.5121 |
| Total | 890337 |
Variants binned by imputation INFO score
Bar chart displaying binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.3 | 25256 | 2.8367 |
| 0.4 | 26183 | 2.9408 |
| 0.5 | 33282 | 3.7381 |
| 0.6 | 50585 | 5.6816 |
| 0.7 | 80223 | 9.0104 |
| 0.8 | 134556 | 15.1129 |
| 0.9 | 538291 | 60.4592 |
| 1.0 | 1961 | 0.2203 |
| Total | 890337 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by alternate allele frequency
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 599161 | 61.5987 |
| 0.1 | 101636 | 10.4490 |
| 0.2 | 64623 | 6.6438 |
| 0.3 | 50350 | 5.1764 |
| 0.4 | 38242 | 3.9316 |
| 0.5 | 32124 | 3.3026 |
| 0.6 | 29075 | 2.9891 |
| 0.7 | 22781 | 2.3421 |
| 0.8 | 21154 | 2.1748 |
| 0.9 | 13539 | 1.3919 |
| Total | 972685 |
Variants binned by imputation INFO score
Bar chart displaying binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.3 | 25532 | 2.6249 |
| 0.4 | 27549 | 2.8323 |
| 0.5 | 33386 | 3.4324 |
| 0.6 | 50924 | 5.2354 |
| 0.7 | 82457 | 8.4773 |
| 0.8 | 141611 | 14.5588 |
| 0.9 | 608974 | 62.6075 |
| 1.0 | 2252 | 0.2315 |
| Total | 972685 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by alternate allele frequency
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 503678 | 60.9229 |
| 0.1 | 87367 | 10.5676 |
| 0.2 | 56248 | 6.8035 |
| 0.3 | 42532 | 5.1445 |
| 0.4 | 34735 | 4.2014 |
| 0.5 | 29219 | 3.5342 |
| 0.6 | 24753 | 2.9940 |
| 0.7 | 20374 | 2.4644 |
| 0.8 | 16736 | 2.0243 |
| 0.9 | 11104 | 1.3431 |
| Total | 826746 |
Variants binned by imputation INFO score
Bar chart displaying binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.3 | 21536 | 2.6049 |
| 0.4 | 22665 | 2.7415 |
| 0.5 | 28263 | 3.4186 |
| 0.6 | 43580 | 5.2713 |
| 0.7 | 70689 | 8.5503 |
| 0.8 | 119657 | 14.4732 |
| 0.9 | 518040 | 62.6601 |
| 1.0 | 2316 | 0.2801 |
| Total | 826746 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by alternate allele frequency
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 500120 | 60.3197 |
| 0.1 | 81317 | 9.8077 |
| 0.2 | 60192 | 7.2598 |
| 0.3 | 45757 | 5.5188 |
| 0.4 | 33589 | 4.0512 |
| 0.5 | 27601 | 3.3290 |
| 0.6 | 25000 | 3.0153 |
| 0.7 | 21926 | 2.6445 |
| 0.8 | 19956 | 2.4069 |
| 0.9 | 13658 | 1.6473 |
| Total | 829116 |
Variants binned by imputation INFO score
Bar chart displaying binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.3 | 20642 | 2.4896 |
| 0.4 | 22159 | 2.6726 |
| 0.5 | 27962 | 3.3725 |
| 0.6 | 42232 | 5.0936 |
| 0.7 | 69216 | 8.3482 |
| 0.8 | 119911 | 14.4625 |
| 0.9 | 525378 | 63.3660 |
| 1.0 | 1616 | 0.1949 |
| Total | 829116 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by alternate allele frequency
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 466444 | 61.6107 |
| 0.1 | 76336 | 10.0829 |
| 0.2 | 52145 | 6.8876 |
| 0.3 | 40115 | 5.2986 |
| 0.4 | 31571 | 4.1701 |
| 0.5 | 24957 | 3.2965 |
| 0.6 | 22185 | 2.9303 |
| 0.7 | 18511 | 2.4450 |
| 0.8 | 15347 | 2.0271 |
| 0.9 | 9472 | 1.2511 |
| Total | 757083 |
Variants binned by imputation INFO score
Bar chart displaying binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.3 | 19423 | 2.5655 |
| 0.4 | 20444 | 2.7004 |
| 0.5 | 25519 | 3.3707 |
| 0.6 | 39305 | 5.1916 |
| 0.7 | 63240 | 8.3531 |
| 0.8 | 108124 | 14.2817 |
| 0.9 | 478849 | 63.2492 |
| 1.0 | 2179 | 0.2878 |
| Total | 757083 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by alternate allele frequency
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 455063 | 60.5522 |
| 0.1 | 79071 | 10.5214 |
| 0.2 | 52713 | 7.0142 |
| 0.3 | 40753 | 5.4227 |
| 0.4 | 32713 | 4.3529 |
| 0.5 | 26387 | 3.5111 |
| 0.6 | 21899 | 2.9140 |
| 0.7 | 17772 | 2.3648 |
| 0.8 | 15079 | 2.0065 |
| 0.9 | 10072 | 1.3402 |
| Total | 751522 |
Variants binned by imputation INFO score
Bar chart displaying binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.3 | 17810 | 2.3699 |
| 0.4 | 18605 | 2.4756 |
| 0.5 | 22930 | 3.0511 |
| 0.6 | 35134 | 4.6750 |
| 0.7 | 56158 | 7.4726 |
| 0.8 | 96863 | 12.8889 |
| 0.9 | 499264 | 66.4337 |
| 1.0 | 4758 | 0.6331 |
| Total | 751522 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by alternate allele frequency
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 403104 | 60.6249 |
| 0.1 | 68447 | 10.2941 |
| 0.2 | 48427 | 7.2832 |
| 0.3 | 35171 | 5.2895 |
| 0.4 | 29621 | 4.4549 |
| 0.5 | 23629 | 3.5537 |
| 0.6 | 18868 | 2.8377 |
| 0.7 | 15855 | 2.3845 |
| 0.8 | 12604 | 1.8956 |
| 0.9 | 9189 | 1.3820 |
| Total | 664915 |
Variants binned by imputation INFO score
Bar chart displaying binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.3 | 17744 | 2.6686 |
| 0.4 | 18556 | 2.7907 |
| 0.5 | 23520 | 3.5373 |
| 0.6 | 36488 | 5.4876 |
| 0.7 | 58537 | 8.8037 |
| 0.8 | 98323 | 14.7873 |
| 0.9 | 410599 | 61.7521 |
| 1.0 | 1148 | 0.1727 |
| Total | 664915 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by alternate allele frequency
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 395977 | 61.5019 |
| 0.1 | 64862 | 10.0742 |
| 0.2 | 44860 | 6.9675 |
| 0.3 | 31946 | 4.9618 |
| 0.4 | 27650 | 4.2945 |
| 0.5 | 22651 | 3.5181 |
| 0.6 | 18438 | 2.8637 |
| 0.7 | 15888 | 2.4677 |
| 0.8 | 13288 | 2.0639 |
| 0.9 | 8285 | 1.2868 |
| Total | 643845 |
Variants binned by imputation INFO score
Bar chart displaying binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.3 | 16822 | 2.6127 |
| 0.4 | 18286 | 2.8401 |
| 0.5 | 22441 | 3.4855 |
| 0.6 | 33312 | 5.1739 |
| 0.7 | 54022 | 8.3905 |
| 0.8 | 91399 | 14.1958 |
| 0.9 | 405739 | 63.0181 |
| 1.0 | 1824 | 0.2833 |
| Total | 643845 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by alternate allele frequency
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 307800 | 61.4667 |
| 0.1 | 55164 | 11.0161 |
| 0.2 | 32490 | 6.4882 |
| 0.3 | 25233 | 5.0390 |
| 0.4 | 20477 | 4.0892 |
| 0.5 | 16167 | 3.2285 |
| 0.6 | 14541 | 2.9038 |
| 0.7 | 11845 | 2.3654 |
| 0.8 | 9815 | 1.9600 |
| 0.9 | 7227 | 1.4432 |
| Total | 500759 |
Variants binned by imputation INFO score
Bar chart displaying binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.3 | 13608 | 2.7175 |
| 0.4 | 14175 | 2.8307 |
| 0.5 | 17406 | 3.4759 |
| 0.6 | 27802 | 5.5520 |
| 0.7 | 45026 | 8.9916 |
| 0.8 | 75930 | 15.1630 |
| 0.9 | 306137 | 61.1346 |
| 1.0 | 675 | 0.1348 |
| Total | 500759 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by alternate allele frequency
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 348878 | 60.6251 |
| 0.1 | 60094 | 10.4426 |
| 0.2 | 40186 | 6.9832 |
| 0.3 | 28433 | 4.9408 |
| 0.4 | 25343 | 4.4039 |
| 0.5 | 20778 | 3.6106 |
| 0.6 | 16672 | 2.8971 |
| 0.7 | 14265 | 2.4789 |
| 0.8 | 12772 | 2.2194 |
| 0.9 | 8047 | 1.3983 |
| Total | 575468 |
Variants binned by imputation INFO score
Bar chart displaying binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.3 | 14213 | 2.4698 |
| 0.4 | 15286 | 2.6563 |
| 0.5 | 19006 | 3.3027 |
| 0.6 | 28720 | 4.9907 |
| 0.7 | 47410 | 8.2385 |
| 0.8 | 84393 | 14.6651 |
| 0.9 | 365311 | 63.4807 |
| 1.0 | 1129 | 0.1962 |
| Total | 575468 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by alternate allele frequency
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 351679 | 61.0500 |
| 0.1 | 57668 | 10.0109 |
| 0.2 | 36584 | 6.3508 |
| 0.3 | 31056 | 5.3912 |
| 0.4 | 24637 | 4.2769 |
| 0.5 | 20528 | 3.5636 |
| 0.6 | 18376 | 3.1900 |
| 0.7 | 14195 | 2.4642 |
| 0.8 | 12601 | 2.1875 |
| 0.9 | 8727 | 1.5150 |
| Total | 576051 |
Variants binned by imputation INFO score
Bar chart displaying binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.3 | 14265 | 2.4763 |
| 0.4 | 14464 | 2.5109 |
| 0.5 | 17905 | 3.1082 |
| 0.6 | 29265 | 5.0803 |
| 0.7 | 49471 | 8.5880 |
| 0.8 | 84042 | 14.5893 |
| 0.9 | 364864 | 63.3388 |
| 1.0 | 1775 | 0.3081 |
| Total | 576051 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by alternate allele frequency
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 335336 | 61.1449 |
| 0.1 | 55733 | 10.1623 |
| 0.2 | 35698 | 6.5091 |
| 0.3 | 29802 | 5.4341 |
| 0.4 | 24023 | 4.3803 |
| 0.5 | 18941 | 3.4537 |
| 0.6 | 15691 | 2.8611 |
| 0.7 | 12679 | 2.3119 |
| 0.8 | 12796 | 2.3332 |
| 0.9 | 7729 | 1.4093 |
| Total | 548428 |
Variants binned by imputation INFO score
Bar chart displaying binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.3 | 14335 | 2.6138 |
| 0.4 | 15353 | 2.7995 |
| 0.5 | 19306 | 3.5202 |
| 0.6 | 29239 | 5.3314 |
| 0.7 | 47692 | 8.6961 |
| 0.8 | 81507 | 14.8619 |
| 0.9 | 339827 | 61.9638 |
| 1.0 | 1169 | 0.2132 |
| Total | 548428 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by alternate allele frequency
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 252967 | 60.0544 |
| 0.1 | 42959 | 10.1985 |
| 0.2 | 28152 | 6.6833 |
| 0.3 | 22830 | 5.4198 |
| 0.4 | 17214 | 4.0866 |
| 0.5 | 15861 | 3.7654 |
| 0.6 | 12687 | 3.0119 |
| 0.7 | 11368 | 2.6988 |
| 0.8 | 9625 | 2.2850 |
| 0.9 | 7567 | 1.7964 |
| Total | 421230 |
Variants binned by imputation INFO score
Bar chart displaying binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.3 | 10665 | 2.5319 |
| 0.4 | 11308 | 2.6845 |
| 0.5 | 13975 | 3.3177 |
| 0.6 | 21938 | 5.2081 |
| 0.7 | 36328 | 8.6243 |
| 0.8 | 60120 | 14.2725 |
| 0.9 | 265811 | 63.1035 |
| 1.0 | 1085 | 0.2576 |
| Total | 421230 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by alternate allele frequency
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 225360 | 61.1662 |
| 0.1 | 39218 | 10.6444 |
| 0.2 | 25744 | 6.9873 |
| 0.3 | 18163 | 4.9297 |
| 0.4 | 15305 | 4.1540 |
| 0.5 | 11643 | 3.1601 |
| 0.6 | 9989 | 2.7112 |
| 0.7 | 9574 | 2.5985 |
| 0.8 | 7715 | 2.0940 |
| 0.9 | 5728 | 1.5547 |
| Total | 368439 |
Variants binned by imputation INFO score
Bar chart displaying binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.3 | 9648 | 2.6186 |
| 0.4 | 10025 | 2.7209 |
| 0.5 | 12805 | 3.4755 |
| 0.6 | 19918 | 5.4061 |
| 0.7 | 31315 | 8.4994 |
| 0.8 | 53791 | 14.5997 |
| 0.9 | 230266 | 62.4977 |
| 1.0 | 671 | 0.1821 |
| Total | 368439 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by alternate allele frequency
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 200558 | 61.3295 |
| 0.1 | 32285 | 9.8726 |
| 0.2 | 22719 | 6.9473 |
| 0.3 | 17282 | 5.2847 |
| 0.4 | 13678 | 4.1827 |
| 0.5 | 11867 | 3.6289 |
| 0.6 | 8875 | 2.7139 |
| 0.7 | 7834 | 2.3956 |
| 0.8 | 6802 | 2.0800 |
| 0.9 | 5117 | 1.5648 |
| Total | 327017 |
Variants binned by imputation INFO score
Bar chart displaying binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.3 | 9764 | 2.9858 |
| 0.4 | 10936 | 3.3442 |
| 0.5 | 14005 | 4.2827 |
| 0.6 | 20565 | 6.2887 |
| 0.7 | 30915 | 9.4536 |
| 0.8 | 51404 | 15.7191 |
| 0.9 | 188941 | 57.7771 |
| 1.0 | 487 | 0.1489 |
| Total | 327017 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by alternate allele frequency
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 219924 | 61.7102 |
| 0.1 | 37324 | 10.4730 |
| 0.2 | 22878 | 6.4195 |
| 0.3 | 18914 | 5.3072 |
| 0.4 | 14273 | 4.0050 |
| 0.5 | 12376 | 3.4727 |
| 0.6 | 10636 | 2.9844 |
| 0.7 | 9420 | 2.6432 |
| 0.8 | 6691 | 1.8775 |
| 0.9 | 3946 | 1.1072 |
| Total | 356382 |
Variants binned by imputation INFO score
Bar chart displaying binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.3 | 10176 | 2.8554 |
| 0.4 | 11351 | 3.1851 |
| 0.5 | 14196 | 3.9834 |
| 0.6 | 23117 | 6.4866 |
| 0.7 | 36687 | 10.2943 |
| 0.8 | 61945 | 17.3816 |
| 0.9 | 198572 | 55.7189 |
| 1.0 | 338 | 0.0948 |
| Total | 356382 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by alternate allele frequency
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 186903 | 61.0375 |
| 0.1 | 30482 | 9.9546 |
| 0.2 | 22899 | 7.4782 |
| 0.3 | 15799 | 5.1595 |
| 0.4 | 12992 | 4.2428 |
| 0.5 | 11416 | 3.7282 |
| 0.6 | 8981 | 2.9330 |
| 0.7 | 8023 | 2.6201 |
| 0.8 | 5784 | 1.8889 |
| 0.9 | 2931 | 0.9572 |
| Total | 306210 |
Variants binned by imputation INFO score
Bar chart displaying binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.3 | 10161 | 3.3183 |
| 0.4 | 11530 | 3.7654 |
| 0.5 | 15377 | 5.0217 |
| 0.6 | 22066 | 7.2062 |
| 0.7 | 33041 | 10.7903 |
| 0.8 | 51728 | 16.8930 |
| 0.9 | 161909 | 52.8752 |
| 1.0 | 398 | 0.1300 |
| Total | 306210 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by alternate allele frequency
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 197652 | 60.4206 |
| 0.1 | 34190 | 10.4516 |
| 0.2 | 23586 | 7.2100 |
| 0.3 | 17549 | 5.3646 |
| 0.4 | 13970 | 4.2705 |
| 0.5 | 11147 | 3.4075 |
| 0.6 | 8972 | 2.7427 |
| 0.7 | 8473 | 2.5901 |
| 0.8 | 6777 | 2.0717 |
| 0.9 | 4811 | 1.4707 |
| Total | 327127 |
Variants binned by imputation INFO score
Bar chart displaying binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.3 | 9559 | 2.9221 |
| 0.4 | 9756 | 2.9823 |
| 0.5 | 13379 | 4.0898 |
| 0.6 | 20193 | 6.1728 |
| 0.7 | 30613 | 9.3581 |
| 0.8 | 51927 | 15.8737 |
| 0.9 | 191258 | 58.4660 |
| 1.0 | 442 | 0.1351 |
| Total | 327127 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by alternate allele frequency
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 152491 | 60.3841 |
| 0.1 | 29173 | 11.5521 |
| 0.2 | 19004 | 7.5253 |
| 0.3 | 13012 | 5.1526 |
| 0.4 | 9659 | 3.8248 |
| 0.5 | 8987 | 3.5587 |
| 0.6 | 6982 | 2.7648 |
| 0.7 | 5992 | 2.3727 |
| 0.8 | 4643 | 1.8386 |
| 0.9 | 2592 | 1.0264 |
| Total | 252535 |
Variants binned by imputation INFO score
Bar chart displaying binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.3 | 7928 | 3.1394 |
| 0.4 | 9305 | 3.6846 |
| 0.5 | 12531 | 4.9621 |
| 0.6 | 18816 | 7.4508 |
| 0.7 | 27942 | 11.0646 |
| 0.8 | 43959 | 17.4071 |
| 0.9 | 131599 | 52.1112 |
| 1.0 | 455 | 0.1802 |
| Total | 252535 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by alternate allele frequency
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 158874 | 61.4177 |
| 0.1 | 27379 | 10.5842 |
| 0.2 | 17762 | 6.8665 |
| 0.3 | 13664 | 5.2822 |
| 0.4 | 11040 | 4.2679 |
| 0.5 | 8826 | 3.4120 |
| 0.6 | 7641 | 2.9539 |
| 0.7 | 5931 | 2.2928 |
| 0.8 | 4665 | 1.8034 |
| 0.9 | 2896 | 1.1195 |
| Total | 258678 |
Variants binned by imputation INFO score
Bar chart displaying binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.3 | 7360 | 2.8452 |
| 0.4 | 7708 | 2.9798 |
| 0.5 | 10549 | 4.0780 |
| 0.6 | 16386 | 6.3345 |
| 0.7 | 25257 | 9.7639 |
| 0.8 | 41642 | 16.0980 |
| 0.9 | 149486 | 57.7884 |
| 1.0 | 290 | 0.1121 |
| Total | 258678 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by alternate allele frequency
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 90190 | 58.7385 |
| 0.1 | 15933 | 10.3768 |
| 0.2 | 10515 | 6.8482 |
| 0.3 | 8531 | 5.5560 |
| 0.4 | 7459 | 4.8579 |
| 0.5 | 5994 | 3.9037 |
| 0.6 | 4942 | 3.2186 |
| 0.7 | 4633 | 3.0174 |
| 0.8 | 3885 | 2.5302 |
| 0.9 | 1463 | 0.9528 |
| Total | 153545 |
Variants binned by imputation INFO score
Bar chart displaying binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.3 | 4470 | 2.9112 |
| 0.4 | 4608 | 3.0011 |
| 0.5 | 6455 | 4.2040 |
| 0.6 | 9979 | 6.4991 |
| 0.7 | 14880 | 9.6910 |
| 0.8 | 24890 | 16.2102 |
| 0.9 | 88077 | 57.3623 |
| 1.0 | 186 | 0.1211 |
| Total | 153545 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by alternate allele frequency
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 91651 | 60.7628 |
| 0.1 | 15815 | 10.4850 |
| 0.2 | 10903 | 7.2285 |
| 0.3 | 8186 | 5.4272 |
| 0.4 | 6623 | 4.3909 |
| 0.5 | 5318 | 3.5257 |
| 0.6 | 4528 | 3.0020 |
| 0.7 | 3882 | 2.5737 |
| 0.8 | 2617 | 1.7350 |
| 0.9 | 1311 | 0.8692 |
| Total | 150834 |
Variants binned by imputation INFO score
Bar chart displaying binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.3 | 5032 | 3.3361 |
| 0.4 | 5445 | 3.6099 |
| 0.5 | 6848 | 4.5401 |
| 0.6 | 11019 | 7.3054 |
| 0.7 | 15840 | 10.5016 |
| 0.8 | 25721 | 17.0525 |
| 0.9 | 80781 | 53.5562 |
| 1.0 | 148 | 0.0981 |
| Total | 150834 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by alternate allele frequency
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 214654 | 62.0407 |
| 0.1 | 34814 | 10.0622 |
| 0.2 | 22927 | 6.6265 |
| 0.3 | 17823 | 5.1513 |
| 0.4 | 13947 | 4.0311 |
| 0.5 | 11380 | 3.2891 |
| 0.6 | 10170 | 2.9394 |
| 0.7 | 10033 | 2.8998 |
| 0.8 | 6059 | 1.7512 |
| 0.9 | 4182 | 1.2087 |
| Total | 345989 |
Variants binned by imputation INFO score
Bar chart displaying binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.3 | 14175 | 4.0970 |
| 0.4 | 16049 | 4.6386 |
| 0.5 | 19662 | 5.6828 |
| 0.6 | 26508 | 7.6615 |
| 0.7 | 34556 | 9.9876 |
| 0.8 | 53144 | 15.3600 |
| 0.9 | 180529 | 52.1777 |
| 1.0 | 1366 | 0.3948 |
| Total | 345989 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering